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Activity Number:
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116
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Type:
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Contributed
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Date/Time:
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Monday, August 7, 2006 : 8:30 AM to 10:20 AM
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Sponsor:
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IMS
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| Abstract - #305406 |
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Title:
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Determination of Differentially Expressed Features in a Combined LC-MS and LC-MS/MS Proteomics Work Flow
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Author(s):
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Olga Vitek*+ and Andrew Garbutt and Ruedi Aebersold
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Companies:
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Institute for Systems Biology and Institute for Systems Biology and Institute for Molecular Systems Biology
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Address:
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1441 N. 34th Street, Seattle, WA, 98103,
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Keywords:
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proteomics ; mass spectrometry ; biomarker discovery ; sample size ; differential expression ; correlation
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Abstract:
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Liquid chromatography coupled to mass spectrometry (LC-MS and LC-MS/MS) is used increasingly for global protein profiling. However, reliable and reproducible analysis of these data is challenging. LC-MS spectra are sensitive in quantifying the abundance of features, but yield features with unknown identities and many false positives. LC-MS/MS approach is specific in sequences identification, but fails to detect many of the features. We combine the advantages of LC-MS and LC-MS/MS approaches in a statistical framework for determination of differentially expressed features. We use identities of MS/MS peaks and shared abundance profiles to account for correlation structure in the data. We also discuss aspects of experimental design---particularly choices of sample size---for mass spectrometry-based experiments. Finally, we illustrate our approach using two complex biological samples.
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